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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;"><span style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px; background-color: rgb(255, 255, 255);">Dear Rens and Carlson,</span>
<div><span style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px; background-color: rgb(255, 255, 255);">I would like to comment on Rens' question on adding transcript data into your annotation. Since I have no access to
google groups, I try to contact you both via mail with, hopefully, the correct mail addresses.</span></div>
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<div><span style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px; background-color: rgb(255, 255, 255);">I have tested Maker-P with multiple parameters, optimized 2 gene prediction tools (SNAP and augustus). Both give similarly
results at which maker find around 17000 gene annotations. I also have RNAseq samples, and as a test case I also used Cufflinks output and processed with TransDecoder to select gene annotations. By using this approach, I end up with 25000 gene annotations.
More or less, all the genes that Maker selected were also selected by the TransDecoder approach. So is it wise to include the information on the 8000 missing genes, based on optimized gene models? probably, there will some false positive in these 8000 missing
genes, but with good criteria and models, it would maybe possible that maker can find more genes annotations.</span></div>
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<div><span style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px; background-color: rgb(255, 255, 255);">Best regards</span></div>
<div><span style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px; background-color: rgb(255, 255, 255);">Arne</span></div>
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<div><span style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px; background-color: rgb(255, 255, 255);">Hi maker team, </span><br style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px; background-color: rgb(255, 255, 255);">
<br style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px; background-color: rgb(255, 255, 255);">
<span style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px; background-color: rgb(255, 255, 255);">I am currently working on a project where we want to incorporate quite a lot of RNA-seq into our annotation. Currently I
see two options: </span><br style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px; background-color: rgb(255, 255, 255);">
<br style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px; background-color: rgb(255, 255, 255);">
<span style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px; background-color: rgb(255, 255, 255);">Provide the cufflinks output as EST-gff </span><br style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px; background-color: rgb(255, 255, 255);">
<span style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px; background-color: rgb(255, 255, 255);">Process cufflinks output with TransDecoder (find ORFs, annotate UTR, etc) and provide this as either pred_gff or model_gff </span><br style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px; background-color: rgb(255, 255, 255);">
<br style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px; background-color: rgb(255, 255, 255);">
<span style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px; background-color: rgb(255, 255, 255);">What would you suggest, and what would be the required formatting for both options? </span><br style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px; background-color: rgb(255, 255, 255);">
<br style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px; background-color: rgb(255, 255, 255);">
<span style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px; background-color: rgb(255, 255, 255);">Thanks in advance, </span><br style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px; background-color: rgb(255, 255, 255);">
<br style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px; background-color: rgb(255, 255, 255);">
<span style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px; background-color: rgb(255, 255, 255);">Rens Holmer </span></div>
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